Not Sure About SURE?

McGill’s Summer Undergraduate Research in Engineering (SURE) Award gives undergraduate students a 16-week, full-time internship position at an engineering research lab at McGill. Awarded as a scholarship, recipients receive an endowment valued at a minimum of $5,625 and the opportunity to work at a lab for the summer.

The 2018 SURE Application period opened on 16 January, initiated by an information session held on the same day. This year, the Faculty of Engineering is offering 125 awards: a substantial jump from the 90 offered last year. The decade-old program is funded by the NSERC Undergraduate Summer Research Award Program, the Faculty of Engineering, the Trottier Institute for Sustainable Engineering and Design, and other donors.


The “summer research traineeships” provide students with exposure to research and the graduate school experience. For the first time ever, SURE will also be recognized with an entry on students’ transcripts.

SURE participants work on one of the many research projects associated with the program. The research projects for 2018 were posted on the Faculty of Engineering website on 16 January. There are projects from the Departments of Architecture, Bioengineering, Chemical Engineering, Civil Engineering, Electrical and Computer Engineering, Mechanical Engineering, Mining and Materials Engineering, and Urban Planning. Each project has an associated professor, and some require a minimum study year.

Application Process

Interested students need to contact the supervising professors of the projects they are interested in, to a maximum of 3 projects. Supervisors must first agree that the student should apply to the project before the student can complete the Online Student Application.

Once the student has filled out the application, they will submit it to their selected supervisor. The deadline to apply is 26 January 2018, and the first round of awards will be announced after 19 February.

If you would like more information about SURE, or to access its application, please visit the Faculty of Engineering’s website here.


Soup and Science: Bringing students close to the research

Feature Photo: From McGill University’s Facebook Page

In the beginning of each semester, the Faculty of Science organizes Soup and Science, a week where professors in different departments discuss their current research. Each day features four or five professors, in fields such as (but definitely not limited to) biochemistry, mathematics, management, psychology, and geography. Each professor is given the opportunity to summarize their research in three minutes.

This is an opportunity for undergraduate students, specifically those in U0 and U1, to understand what “research in a research-intensive university is all about”. Listening to talks on the cutting-edge research conducted at McGill allows students to bridge the link between the foundational information they learn in classes with research and the future of their respective fields.

This semester, Soup and Science is running from January 15 – 19 at 11:30-12:30 every day at the Redpath museum. Students should come early, since spaces fill up quickly.

On Wednesday, January 17th, Suzanne Fortier, the President of McGill University, was a special guest to this series of mini-talks. The talks opened up with the perspective of a student, followed by five McGill professors, and concluded with a series of questions about the talks. After the presentations, students are offered free soup and sandwiches.

Sasha McDowell (Final year Honours Biology student)

Sasha McDowell is an international student who is strongly interested in understanding more about her field. In her second year at McGill, she began working in a molecular biology laboratory during the school year. After taking BIOL 306, Neural Basis of Behaviour, she found herself so interested in the course topic that she began working in the Watt Lab on a SURE scholarship over the summer. In these sixteen weeks of work, she worked with mice and tested potential therapies of human ataxia diseases. Wanting to gain insight into all the aspects of research, she took a field course where work was conducted Mont. Saint-Hilaire. McDowell described the value she found in discovering all the avenues that research consists of.

Professor Nii Addy (Desautels Faculty of Management)

Professor Nii Addy completed an undergraduate degree in Engineering before beginning his work in Management. His work focuses in the cross-sector partnership between different organizations to solve complex societal problems. He showed the group an example of a complex problem; the increase of obesity rates among US adults from 1990 to 2006. In order to solve this systemic problem, it is important to consider a “multiplicity of perspectives”. He described the impact of minor changes, such as proximity, on major changes, the commonplace of obesity in North America. Professor Addy currently works with a “multidimensional proximity framework” to help solve complex societal issues.

Professor Kevin Manaugh (Dept. of Geography, McGill School of Environment, Associate of the School of Urban Planning)

Professor Manaugh’s work primarily deals with the design of sustainable cities. He showed the group images of cities before city-planning became a profession, in which industry were situated next to homes, child labour was prevalent, and cities were commonly plagued with societal, economic, and environmental problems. Ebenezer Howard blazed the trail for urban planning when wrote a book on the idea of a garden city, where cities were designed with the concept of “separation of uses”. In fact, most of North America has developed around this idea of a garden city. Dr. Manaugh’s work deals with how to best design the urban environment in a way that reduces the environmental impact, increases biodiversity, and includes the voices of marginalized people. In his own words, the vision of his research is to improve human well-being while making cities more resilient, socially inclusive, and having less environmental impact.

Professor Eric McCalla (Dept. of Chemistry)

Dr. McCalla is a new professor at McGill who researches in advanced batteries. He described the usefulness of lithium-ion batteries in our mobile devices and electric vehicles. However, the current state of research has not yet allowed these batteries to be utilized in renewable energy. For this to be done, the lifetime of the batteries need to be increased five fold, and the batteries need a higher energy density. In his lab, Professor McCalla studies the effects of different compositions for the positive electrode, and is hoping to study the possibility of replacing the current, liquid electrolyte, with a more stable solid electrolyte.

Professor Thibault Mesplède (Dept. of Microbiology and Immunology)

Dr. Mesplède’s lab currently study HIV, a virus that is not cured by antiretroviral therapy. He hopes to discover whether viral reservoirs are latent, or persistently replicating in hidden spaces or anatomical sites, much in the way that microbial organisms can be found within the extreme conditions of hot springs or freezing tundra. His lab uses deep sequencing to reconstruct viral evolution and the phylogeny of HIV.

Professor Jackie Vogel (Dept. of Biology, Associate professor in Computer Science)

By training, Dr. Vogel is a chemist and a biologist. However, her lab is truly interdisciplinary, using techniques from mathematics and computer science to mine data from biological systems. She currently focuses on the “gaps of knowledge that are particularly interesting”. More specifically, she wishes to find the mechanism that occurs from prophase to prometaphase in mitosis. Spindle pole bodies need to be perfectly aligned along a certain axis in order to replicate properly. She uses a basic projection from linear algebra to determine whether or not the cells have aligned their spindles. By studying a mutant that fails to do so, she is currently working on quantitatively analyzing and visualizing this step in mitosis.

Research Awareness Day 2017

November 25th, 2017 marked the annual Research Awareness Day (RAD) held by the Biochemistry Undergraduate Society (BUGS). One of the most prominent undergraduate research events of the year with over 80 undergraduate attendees, RAD featured a full day of rapid-fire presentations by 10 different biochemistry professors, lunch, and a poster fair featuring graduate and undergraduate students alike. With the diversity in the research topics of the different professors, there was something for everybody, not just those majoring in biochemistry.

Once again, RAD 2017 was a great event to learn more about research, network with profs, and to get excited about science. You definitely do not want to miss out on RAD if you have the chance, but for those that didn’t make it to RAD 2017, here’s a glimpse at what the professors talked about:

Dr. Albert Berghuis

As the chair of the biochemistry department, Dr. Berghuis gave a brief snapshot of biochemistry at McGill, past (biochemistry is one of the oldest departments at McGill!) and present, before presenting his lab and his current research. The Berghuis lab centers around structural biology and drugs: the development of anti-cancer drugs, the identification of fungal drug targets, and various other drug related topics. But no topic is as pressing as the central feature of the Berghuis lab: antibiotic resistance. Taking a structural biology approach, using techniques such as x-ray diffraction, NMR, scattering, and electron microscopy, the lab seeks to use structures of bacterial enzymes that confer antibiotic resistance to develop new, better antibiotics.

Dr. Jose Teodoro

The Teodoro lab is in equal parts biochemistry and virology, as their primary focus is to learn how to kill cancer cells using viruses that only seem to kill cancer cells by honing in on specific cellular features that only cancer cells possess. For example, the chicken anaemia virus, which causes anaemia in chickens, only targets and kills rapidly dividing cells by interacting with the Anaphase Promoting Complex/Cyclosome. While this destroys chicken hematopoietic stem cells, it is fantastic news for cancer biologists since cancer cells also tend to divide rapidly. Furthermore,the chicken anaemia virus is small, and its only function is to target and destroy rapidly dividing cells. The Teodoro lab also works on p53, a very well known gene that encodes a tumour-suppressing transcription factor, and its effects on tumor angiogenesis.

Dr. Ian Watson

The Watson lab focuses on melanocyte biology in melanoma. 50% of melanomas have a hotspot mutation BRAF, and 25% have a hotspot mutation in NRAS, both of which are mitogen-activated protein kinase (MAPK) regulators, and are druggable targets. The goal of the lab is to develop a therapeutic strategy for long-term survival, as many current techniques show initial promise but no increase in the rates of long-term survival. The Watson lab created stable Cas9-encoding mice with which genome manipulation can be easily done, and they also collect samples from patients who underwent checkpoint inhibition therapy, so they have excellent models for melanoma, the poster child for precision therapy of the future.

Dr. Alba Guarné

One of the newest additions to the McGill biochemistry department, hailing from McMaster University, the Guarné lab studies genome stability and DNA-protein interactions. DNA needs to be extremely condensed to fit into the tiny nucleus of the cell. Almost all DNA processes require the DNA to be decondensed. Once this occurs, the DNA is under constant attack by many components of the cell. Over time, this constant attack can lead to significant mutations in the DNA if it weren’t for the DNA repair mechanisms that prevented the accumulation of mutations. One of the projects the Guarné lab is currently undertaking is the analysis of DNA mismatch repair, specifically studying how the mechanism can discern which of the two DNA strands contain the mutation. All this is done through structural biological techniques such as x-ray diffraction and EM microscopy.

Dr. Janusz Rak

The Rak lab, at the Montreal Children’s Hospital, is a cancer and angiogenesis laboratory, asking questions related to the complexities of diseases. One disease the Rak lab studies specifically is glioblastoma, a type of brain cancer that kills nearly 100% of patients due to the tendency for the tumour to hemorrhage in the brain, and its peculiar penchant of forming blood clots elsewhere, such as the leg, demonstrating the interactivity of cancer. The lab is interested in the unconventionally connectivities of cells — one that does not involve neither the neural nor the endocrine system. Glioblastoma cells exemplify this lack of convention as they seem to communicate using extracellular vesicles, which Dr. Rak described as “motherships that can change things in different ways”. Techniques used in Dr. Rak’s lab include atomic force microscopy and liquid biopsy.

Dr. Uri David Akavia

The Akavia lab is interested in metabolism bioinformatics in cancer, conducting computer modelling of the metabolism of the entire cell, specifically in cancer cells. The lab also intentionally changes genes known to be involved in metabolism using Cas9, and observes and models the consequences. (This leads to some pretty wild flow charts). Ultimately, the Akavia lab seeks to examine how cancer metabolism makes the cell resistant to treatment or developing cancer, and to develop treatment options from the results.

Dr. Bhushan Nagar

The Nagar lab uses structural biology techniques, specifically x-ray crystallography, to decipher molecular mechanisms that underlie diseases. The lab has a diverse range of research interests, such as analysis of IFIT proteins, members of the innate immunity which interact with viral RNAs to block their replication; AvrA, a bacterial protein that blocks immune signalling in the host cell to promote successful infection by the bacteria; and lysosomal enzymes, a subset of acid hydrolases whose mutations lead to lysosomal storage diseases. The Nagar lab hopes to use information gleaned through structural analysis to develop better therapeutics, such as drugs and pharmaceutical chaperones, for associated diseases.

Dr. Alain Nepveu

The ultimate goal of the Nepveu lab is to develop a novel cancer treatment by exploiting vulnerabilities of the cell (not JUST rapid divisions, but other characteristics as well), as well as examining base excision repair. The Nepveu lab uses mouse models and a lot of different assays to collect the data. Dr. Nepveu also stressed the importance of starting research early, and that you don’t need to have prior research experience to conduct interesting experiments in the lab — the skills you learn from making pizza at your part-time job can be transferred to running a PCR! But ultimately, you should not be shy to approach professors to ask about getting research experience.

Dr. Jason Young

The Young lab’s primary focus is on chaperones, specifically the Hsp70s and 90s, which anyone can learn about in GREAT detail if they take BIOC 212/ANAT 212 from the man himself, but Dr. Young’s RAD presentation was about how to get involved in research, in which he also stressed that you don’t need research experience to get involved in research at the undergraduate level, and that there are many classes such as the 396s and independent research courses available to students, providing a helpful and resourceful end to the rapid-fire talks.

This month on the PDB: December

Hi everybody! 162 structures were released from November 28th to December 5th, ranging from the typical Homo sapiens proteins to the zesty proteins of the Asian rice. Without further ado, let us take some time to peruse this newly released selection of never-before seen macromolecule structures!

  1. HSP90 WITH [sic] indazole derivative, by Graedler, U., Amaral, M., & Schuetz, D.. You know how part of what makes the PDB exciting is that the PDB releases never-before-seen-structures? Well this is not one such case, but just like the lysozymes of last week, this title is notable in that it is actually the name of not one, but SIX separate releases for this week. Hsp90 (heat shock protein 90) is a chaperone protein that promotes the proper folding, stabilization, and activation of a client polypeptide in an ATP-dependent manner, commonly as a dimer. In teaching materials, Hsp90 usually looks like some weird ellipses lumped together to form some two-pronged rabbit head-looking thing, but now you can see what it really looks like, in six slightly different conformations! Indazole derivatives are Hsp90 inhibitors, and these monomeric structures of human Hsp90 are each binding a slightly different indazole derivative. Why are they monomeric and what’s with all these different indazole derivatives? Well, the paper hasn’t been published yet so you’ll have to keep on guessing for a while, but until then, you can entertain yourself by looking at the structures. The PDB accession codes are 5LNY, 5LNZ, 5LO0, 5LO1, 5LO5, and 5LO6. The following figure includes an approximate surface density of the protein, which is why it probably looks a little strange. You can see there are slight differences in conformation between the structures, but for the most part they look decently similar.3.1
  2. Crystal structure of Os79 from O. sativa in complex with UDP, by Wetterhorn, K.M., Gabardi, K., Michlmayr, H., Malachova, A., Busman, M., McCormick, S.P., Berthiller, F., Adam, G., and Rayment, I. This is actually a generalization of the titles of four different structures, all of Os79 from O. sativa in complex with UDP, with and without different mutations and some with different sugar moieties. Oryza sativa, the humble Asian rice, one of the most essential cereal crops to society, is susceptible to head blight infections caused by fungi in the Fusarium genus that affects many other cereal crops as well. Trichothecene toxins are a family of toxins that are responsible for the virulence of Fusarium head blight, and toxic to humans and livestock as well as plants since it inhibits protein synthesis in the eukaryotic ribosome. Os79 is a UDP-glycosyltransferase: it adds a glycosyl moiety to a substrate using a co-substrate such as a UDP-glucose (a glucose bound to a uridine diphosphate). Glycosylating trichothecenes reduces its bioavailability and toxicity, so it would be super rad to engineer a protein that could easily glycosylate these toxins and prevent humanity from losing a lot of crops, some livestock, and a few humans every year. That’s a lot of lives saved! Os79 seems to be a good candidate for this ^type of protein engineering, but this goal is still in the fledgling stages as there are a lot of different trichothecenes and only one Os79 (Remember that enzyme-substrate specificity which we thought made enzymes so cool? Well now it’s sort of biting us in the butt. Enzymes are still cool though, obviously). The good news is that the group that released these structures also did some structural and activity analyses and determined what parts of the structure controlled its specificity. You can read all about it here: The PDB accession codes are 6BK0, 6BK1, 6BK2, and 6BK3.3.2

Someone requested the experimental method metrics of the PDB releases, so here they are: out of 162 structures released this week, 146 were obtained through x-ray diffraction. 4 structures were obtained using cryo-electron microscopy, the up-and-coming technology in the world of structural biology (the 2017 Nobel Prize in Chemistry was awarded to the developers of cryo-EM), a lower number than the usual. This week, there are a whopping 12 structures obtained through solution microscopy. What are these mysterious 12 structures? The 4 cryo-EM structures? The 144 x-ray diffraction structures? (You already saw 2 of them.) Go check them out yourself on this week’s PDB release! You can find it here: Happy lurking!

Battling on the Shoulders of Giants

In the 20th century, we were proposed with two revolutionary theories in physics: quantum mechanics and relativity. Quantum mechanics deals with small scale (molecular/atomic and smaller) behaviour. Max Planck, a German physicist, initiated this field of physics. Some well-known statements of quantum mechanics are that matter can be viewed as a wave which describes the chances of finding it at a given position (proposed by Schrodinger), and that it is impossible to measure a particle’s position and momentum with a low enough uncertainty (proposed by Heisenberg).

In 1915, Einstein published his renowned theory of general relativity. Relativity transformed our understanding of space, time, and gravity, showing that the former two are in fact one continuum, known as spacetime, and gravity is a result of a bend in the geometry of this continuum.

A great thing that Einstein’s relativity predicted was the existence of black holes. Theoretically speaking, any object, when shrunk to a small enough radius (Schwarzchild radius) will collapse into a singularity known as a black hole. Every black hole has a boundary known as the event horizon, past which nothing can escape. If there’s any place in the universe that is truly unreachable, it is past the event horizon of a black hole. There are theories on what happens when one gets past the event horizon, but there doesn’t seem to be a way to prove them.

At the singularity, spacetime and thus all known laws of physics breaks down. Moreover, a black hole’s singularity is large enough that it cannot be ignored from general relativity, but is also small enough that one cannot ignore the effects of quantum mechanics. As it turns out, quantum mechanics and general relativity do not make a great fit together. One main reason for this conflict is the perception of time by either theory. In general theory, time is viewed as dynamic and stretchable, but quantum mechanics views it as fixed and merely there for quantum states to evolve. Hence, physicists are on a quest to unify the two theories by reformulating gravity in terms of quantum mechanical principles. There are quite a few theories that have been described so far, with the most successful being loop quantum gravity theory and string theory. Other theories include spin foam models, causal set theory, and shape dynamics. However, unifying theory has not been discovered yet. It is interesting that two theories that are highly influential and greatly supported by experimental evidence turn out to be incompatible with each other. Hopefully a reformulation of either or both theories will allow us to solve this puzzle in physics very soon.

Undergraduate Research 101

Undergraduate research is one of the most rewarding activities at McGill. Experience in undergraduate research exposes students to scientific inquiry, laboratory procedures, and the graduate school environment. However, as rewarding as research is, if you’re just starting university, securing it may be daunting and unfamiliar.

Fortunately, MSURJ is here to help! The following is our breakdown of undergraduate research: what skills to have, how to apply, and what to do in the lab. After reading our guide, you’ll hopefully have the confidence and knowledge to secure that research position you’ve wanted!

Lesson 1: Preparing a Strong Application

A strong application which displays your best qualities is key when contacting professors for research. Here are some tips on how to make your application stand out.


Research requires more than just technical skills. Some helpful qualities in research include communicationcreativitypersistence, and organization. In particular, creativity is vital when conducting independent research projects. Make sure to emphasize these skills on top of your technical ones when drafting a CV or email.

Get Involved, Attend Events

Research-related events are constantly happening across campus and they’re a great way to meet faculty and talk with professors about their research. Most of the time, professors who attend these events are looking for students to join their labs!

For example, departments often hold Departmental Research Days and Departmental wine and cheeses, while the Faculty of Science holds Soup and Science. You can also attend special research-related events, or stay connected with the Student Research Initiative. Another good way to be in the loop about these events is through SUS and faculty newsletters.

Other Tips

It’s important to be proactive when securing research. Contact more than one professor or researcher because labs are often full, and don’t wait until the last minute! Making contact as early as possible is just as important because labs often fill up quickly.

Secondly, all research labs are relying more and more on programming. Computer software is invaluable for data analysis, visualization, and computational modeling. As a result, knowing how to program adds another skill that will make you useful in the lab. The most common languages in research are Python, MATLAB, ImageJ, C, and R. While you can self-teach yourself these, taking a course such as COMP 202 is a good way to start learning.

Lesson 2: Getting into Research

Now that you have the skills for research, it’s time to find laboratory opportunities. McGill has countless resources to give your research experience, and not all of them involve contacting professors.

Research Opportunities (During the Term)


McGill offers numerous research courses that you can take for credits. Specifically, there are a total of 396 classes that involve supervised research, which you can take with any department in the Faculty of Science, and 466 classes involving independent research, which you must take with your own department in Science.

Honours Programs

If you wish to do a thesis during your undergraduate studies, considering applying for the Honours option of your program, if offered. The Faculties of Science and Engineering offer Honours programs for specific majors.


Finally, if you have demonstrated financial aid, you can secure a work-study position with any faculty that can involve paid research.

Online Resources

There are numerous online resources for finding research opportunities during the term. Professors often post on CAPS, and the Science Faculty has resources on their website as well.

Research Opportunities (Summer)

Faculty of Science and Engineering

Students in the Faculty of Science are eligible for two research awards: the Science Undergraduate Research Award (SURA) and the NSERC Undergraduate Student Research Award (USRA). Students in the Faculty of Engineering also qualify for USRA as well as the Summer Undergraduate Research in Engineering (SURE). All of these awards give its winners a stipend to fund their personal expenses while doing research over the summer.

International Opportunities

Going abroad to do research is a great way to establish oversea connections and expose yourself to different research environments. Some research programs McGill students can apply to include the DAAD Research Internship in Science and Engineering (a German academic exchange), the EPFL Research Internship, and the UTokyo UTRIP Program.

More research opportunities can also be found on the Science Faculty’s website.

Contacting Professors

Make sure to do your homework before contacting professors. This will show that you genuinely care about their research and are eager to join their lab.

We recommend researching potential fields and departments that interest you, and specifically reading the research of the professor you plan on contacting. Scanning the abstracts from their recent publications will really demonstrate that you understand what you’re signing up for. For an even deeper understanding of what the professor’s lab is like, you can talk to other students who have worked in their lab. Make sure to never assume that a professor’s research is closely related to a course that they teach!

Also remember to approach the faculty with respect (address them formally) and understand that they’re busy. It may be best to contact professors during their office hours or via email. However, an in-person exchange can be very valuable, (and professors get swarmed with emails!) so try to schedule a time to talk as a follow-up to your email.

When introducing yourself, talk about your interests, qualifications (coursework and past experience), and your expectations of what the lab will be like. Have your CV and letter of intent available. If possible, try to think of an idea for a project that aligns with the skills of the supervisor you’ve contacted; think about what you want out of the research opportunity.

If a professor informs you that their lab is full, don’t be discouraged! Follow up with questions like when would be a good time to ask again, what skills they are looking for, and what you could work on in the meantime.

Lesson 3: What to do in the Lab

Your first laboratory experience may not be what you expect it to be; research positions can be very self-directed, and your supervisor may not be there to hold your hand through everything. In big labs, you can expect to be working with other graduate students and research assistants. The development of your research skills is up to you, so make sure to demonstrate a genuine interest and initiative. Feel free to have your own interests and discuss them with your supervisors.

Undergraduate research is still a professional position. When you’re working in a lab, always respond quickly to emails, be polite, and be on time. Remember that the research you’re helping with is someone else’s life’s work. If you’re not sure about something in the lab, or if you’re asked if you can do something, never lie. The safest option is to always be honest about what you can do, and show an eagerness to learn.

Keep on Trying!

Don’t expect to receive a yes to your first attempt at securing research. Always work to improve your skills through attending events, keeping updated on your field, and taking relevant courses.

If you’re interested in more research-related events or research publication, make sure to also follow the Abstract and the McGill Science Undergraduate Research Journal!

This week on the PDB: November 24th – November 30th

Welcome back to another week of “This week on the PDB”, where I discuss  you a very small section of new, never-before-seen protein structures uploaded to the Protein Data Bank, because proteins just keep on getting discovered.

  1. Lysozyme is an enzyme essential to our immune system that destroys bacterial cell walls. It is ubiquitous in the body: tears, mucus, blood, you name it, you can probably find lysozyme there. Lysozyme also holds a special place in the PDB, as not only was it the FIRST structure to be deposited in the PDB, back in the day when the whole PDB consisted of only 7 structures, but it is also the protein with the MOST different structures deposited, largely owing to a series of experiments conducted Brian Matthews where he made various (and by “various”, I mean “hundreds of”) mutations to lysozyme. Lysozyme is also one of the most consistently crystallisable proteins and has consequently been used to study the protein crystallization process. This week, lysozyme has once again reared its head on the PDB, where Hosur et al. deposited four new structures of lysozyme, at different time increments in the guanidine hydrochloride and glycerol soaking process. The picture below is of the four structures and the ligands aligned with each other. The PDB accession codes are 5H6A, 5H6C, 5H6D, and 5H6E. The associated article has not been published yet, so it the purpose of this structure is unclear, but be sure to check out all the other hundreds of lysozyme structures on the PDB, which can be accessed here.


    Hen Egg White Lysozyme native crystals soaked in precipitant solution containing 2.5 M guanidine hydrochloride and 25% glycerol.

  2. PolyA polymerase module of the cleavage and polyadenylation factor (CPF) from Saccharomyces cerevisiae. In order for a freshly transcribed piece of RNA to mature into a useful piece of mRNA for translation, its 3’ end must be cleaved, and a string of adenines added to form a polyA tail. CFP mediates this whole process, making it one of the MVPs of mRNA processing, but for some reason, we don’t really know how this amazing complex of proteins so important to our existence assembles itself (shocking, I know. I rank it high in my list of “why don’t we know this” along with the polymerases involved in DNA replication, where there has been ambiguity for quite some time now). At least, until Casañal and Kumar et al. solved the structure of nuclease, polymerase, and phosphatase modules of the CPF in the common baker’s yeast, S. cerevisiae, using electron microscopy with a resolution of 3.55Å. You can read all about the structural features, such as the four beta propellers (ooooohhh), of the yeast—a great model eukaryote—CPF here. The PDB accession code is 6EOJ.


    Cleavage and polyadenylation factor (CPF) from Saccharomyces cerevisiae

  3. Crystal Structure of pro-TGF-beta 1. This structure of the pro-transforming growth factor-beta 1 from the wild boar was obtained through x-ray diffraction by Zhao, B., Xu, S., Dong, X., Lu, C., Springer, T.A. with a resolution of 2.9Å. TGF-beta 1 mediates many cellular functions, including growth, division and proliferation, differentiation, and apoptosis (programmed cell death). It is also important for the immune system, where it can interfere with other cytokines involved in the cellular immune response. In general, it is a very important cellular signalling protein, specifically a cytokine. It also has an implication with tumor development, and consequently holds relevance to cancer (as we all know, anything with connection to cancer is a hotbed of potential biomedical research). This structure has a swap between the N-terminal prodomain and the C-terminal GF domain, which appears to affect how the proteins assemble with each other. The associated article is heavy on the structural biology and lighter in clinical implications, but can be read here. The PDB accession code is 5VQF.2.4

The previous week, a total of 220 structures were released on the PDB. While many of them were simply different resolutions of the same protein (not to mention those four lysozyme structures), there are still a plethora of structures released every week. This just goes to show the expansiveness and diversity in the realm of macromolecules. You can find all the PDB releases this week here: See you next week!